The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma

BACKGROUND: Reference genome and transcriptome assemblies of helminths have reached a level of completion whereby secondary analyses that rely on accurate gene estimation or syntenic relationships can be now conducted with a high level of confidence. Recent public release of the v.3 assembly of the mouse bile-duct tapeworm, Hymenolepis microstoma, provides chromosome-level characterisation of the genome and a stabilised set of protein coding gene models underpinned by bioinformatic and empirical data. However, interactome data have not been produced. Conserved protein-protein interactions in other organisms, termed interologs, can be used to transfer interactions between species, allowing systems-level analysis in non-model organisms. RESULTS: Here, we describe a probabilistic, integrated network of interologs for the H. microstoma proteome, based on conserved protein interactions found in eukaryote model species. Almost a third of the 10,139 gene models in the v.3 assembly could be assigned interaction data and assessment of the resulting network indicates that topologically-important proteins are related to essential cellular pathways, and that the network clusters into biologically meaningful components. Moreover, network parameters are similar to those of single-species interaction networks that we constructed in the same way for S. cerevisiae, C. elegans and H. sapiens, demonstrating that information-rich, system-level analyses can be conducted even on species separated by a large phylogenetic distance from the major model organisms from which most protein interaction evidence is based. Using the interolog network, we then focused on sub-networks of interactions assigned to discrete suites of genes of interest, including signalling components and transcription factors, germline multipotency genes, and genes differentially-expressed between larval and adult worms. Results show not only an expected bias toward highly-conserved proteins, such as components of intracellular signal transduction, but in some cases predicted interactions with transcription factors that aid in identifying their target genes. CONCLUSIONS: With key helminth genomes now complete, systems-level analyses can provide an important predictive framework to guide basic and applied research on helminths and will become increasingly informative as new protein-protein interaction data accumulate

A link between transcription fidelity and pausing in vivo

Pausing by RNA polymerase is a major mechanism that regulates transcription elongation but can cause conflicts with fellow RNA polymerases and other cellular machineries. Here, we summarize our recent finding that misincorporation could be a major source of transcription pausing in vivo, and discuss the role of misincorporation-induced pausing

Scientific Uncertainty and Climate Change Policy

Environmental Economics and Policy,

High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors

The vast majority of organisms possess transcription elongation factors, the functionally similar bacterial Gre and eukaryotic/archaeal TFIIS/TFS. Their main cellular functions are to proofread errors of transcription and to restart elongation via stimulation of RNA hydrolysis by the active centre of RNA polymerase (RNAP). However, a number of taxons lack these factors, including one of the largest and most ubiquitous groups of bacteria, cyanobacteria. Using cyanobacterial RNAP as a model, we investigated alternative mechanisms for maintaining a high fidelity of transcription and for RNAP arrest prevention. We found that this RNAP has very high intrinsic proofreading activity, resulting in nearly as low a level of in vivo mistakes in RNA as Escherichia coli. Features of the cyanobacterial RNAP hydrolysis are reminiscent of the Gre-assisted reaction—the energetic barrier is similarly low, and the reaction involves water activation by a general base. This RNAP is resistant to ubiquitous and most regulatory pausing signals, decreasing the probability to go off-pathway and thus fall into arrest. We suggest that cyanobacterial RNAP has a specific Trigger Loop domain conformation, and isomerises easier into a hydrolytically proficient state, possibly aided by the RNA 3′-end. Cyanobacteria likely passed these features of transcription to their evolutionary descendants, chloroplasts

Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics

The identification of the protein-coding regions of a genome is straightforward due to the universality of start and stop codons. However, the boundaries of the transcribed regions, conditional operon structures, non-coding RNAs and the dynamics of transcription, such as pausing of elongation, are non-trivial to identify, even in the comparatively simple genomes of prokaryotes. Traditional methods for the study of these areas, such as tiling arrays, are noisy, labour-intensive and lack the resolution required for densely-packed bacterial genomes. Recently, deep sequencing has become increasingly popular for the study of the transcriptome due to its lower costs, higher accuracy and single nucleotide resolution. These methods have revolutionised our understanding of prokaryotic transcriptional dynamics. Here, we review the deep sequencing and data analysis techniques that are available for the study of transcription in prokaryotes, and discuss the bioinformatic considerations of these analyses

Epidemiology of Acute Injuries in Surfing: Type, Location, Mechanism, Severity, and Incidence: A Systematic Review

Prospective and retrospective studies have examined traumatic injuries within competitive and recreational surfers worldwide using online surveys and health care facility (HCF; e.g., hospital, emergency department, medical record) data. However, few studies have provided a synthesis of all available literature. The purpose of this study was to obtain, critique and synthesise all literature specific to acute surfing injuries, and evaluate differences in injury type, mechanism and location between HCF and survey data. A systematic literature review design was used to identify relevant articles from three major databases. Peer-reviewed epidemiological studies of musculoskeletal surfing injuries were included. A modified AXIS tool was used for critical appraisal, and objective data was extracted and synthesized by lead researchers. Overall frequencies for injury location, type and mechanism were calculated from raw injury data. A total of 19 cross-sectional articles of fair to good quality (Modified AXIS 54.2–83.3%) were included in this study; 17 were National Health and Medical Research Council (NHMRC) level III-2 (retrospective) and two were level II (prospective). Articles examined competitive, recreational and combined populations. Injury data from Australia, Brazil, UK, USA, Portugal, Japan, Norway, and worldwide were represented. Skin (46.0%; HCF 50.1%, survey 43.8%) and being struck by own surfboard (38.6%; HCF 73.4%, survey 36.7%) were the most common injury type and mechanism. Head, face and neck injuries were most common in HCF (43.1%) versus lower limb injuries (36.4%) in survey data. Incidence proportion was highest in aerialists (0.48). Incidence rate (number of injuries per 1000 h) ranged from 0.74 in Australian surfers (Melbourne) to 6.6 in international contest surfers from medical record data. This review highlights the prevalence of skin, board-related, head, face and neck, and lower limb surfing injuries across available literature. Proposed use of protective equipment and foam-based surfboards in dangerous or crowded surf locations may reduce injury risk

Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase

Transcription in all living organisms is accomplished by multi-subunit RNA polymerases (msRNAPs). msRNAPs are highly conserved in evolution and invariably share a B400 kDa five-subunit catalytic core. Here we characterize a hypothetical B100 kDa single-chain protein, YonO, encoded by the SPb prophage of Bacillus subtilis. YonO shares very distant homology with msRNAPs, but no homology with single-subunit polymerases. We show that despite homology to only a few amino acids of msRNAP, and the absence of most of the conserved domains, YonO is a highly processive DNA-dependent RNA polymerase. We demonstrate that YonO is a bona fide RNAP of the SPb bacteriophage that specifically transcribes its late genes, and thus represents a novel type of bacteriophage RNAPs. YonO and related proteins present in various bacteria and bacteriophages have diverged from msRNAPs before the Last Universal Common Ancestor, and, thus, may resemble the single-subunit ancestor of all msRNAPs

AN ECONOMIC ANALYSIS OF PRODUCT QUALITY WITHIN THE CANADIAN CHEESE INDUSTRY

Food Consumption/Nutrition/Food Safety,